After Beta is defeated by his "younger brother" Gamma following Final Egg, Dr. Robotnik looks set to cast the black robot aside and refuse him a place on the Egg Carrier. Mutely pleading with his creator, Beta eventually extracts the grudging concession that "Okay, okay. We could always use a spare set of parts, I guess". Eggman's words prove unpleasantly prophetic for E-101.

The robot is rediscovered only when Gamma enters the wrong room after being assigned to extract Birdie from Amy's cell. E-102 stumbles in on his older sibling being physically dismembered in an Egg Carrier robotics lab, his legs a sparking pile of scrap on the floor as mechanical arms remake him into into E-101mkII. This witnessing of Robotnik's callous cruelty even towards his own creations is the breaking point that sets Gamma on the road to apostasy; first freeing Amy Rose, then sparing Sonic's life, and eventually deleting Eggman from his registry as lord and master. Gamma's quest now turns to the fratricidal, and after hunting down Delta and Epsilon, he returns to the Egg Carrier for Zeta and finally Beta.

The remade E-101 fights Gamma on the Carrier's central arena; the same spot in which others fight ZERO and Chaos 6. Beta is much stronger and faster in this form; his principal attacks include mass missile-firing and charging forward with his energy shield to slam Gamma. As the battle progresses, Beta takes to flying high above the crashed Carrier and firing exploding energy spheres back down at the deck. The robot's barrier shield makes attacking him from the front a useless endeavour; only after he charges is Gamma given the opportunity to strike, with just enough time to fire a missile at Beta's underprotected back before he turns.

At the very end of the fight, a downed Beta spites his younger brother with a final strike just before he explodes. The attack mortally damages Gamma, who collapses himself only seconds later - his quest to free his brothers finally accomplished. The robot's story does have a bittersweet ending, as it turns out that Beta and Gamma's animalorganic batteries were both part of Birdie's family of Flickies. After Amy destroys ZERO, the trio are happily reunited.